In this paper,ISEA: includes Philippines, Indonesia, and Malaysian Borneo. Taiwan-excluded

Near Oceania (the western Pacific): includes New Guinea, the Bismarck Archipelago, Bougainville, and the Solomon Islands; and

Remote Oceania includes Island Melanesia southeast of the Solomons (including Vanuatu and Fiji), Polynesia, and Micronesia

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Some highlights:

Haplogroup B4a1a, although almost exclusively associated with speakers of Austronesian languages, cannot have dispersed from Taiwan into ISEA and the Pacific 3–4 ka. The 95% confidence limits on the ages of B4a1a1 and B4a1a1a from complete mtDNAs explicitly reject this explanation for their distribution (Table 1). Because B4a1a, along with some haplogroup Q lineages—of likely New Guinean origin, which occur in Polynesia at a rate of <5%[10] and [12]—make up almost all of the mtDNAs found in Polynesia, these results exclude any significant direct Taiwanese contribution from 4 ka to the maternal ancestry of Polynesians. (We cannot entirely rule out an early Holocene dispersal from Taiwan >8 ka,23 but such a dispersal would not match the archaeologically dated “out of Taiwan” model.)

In ruling out both a simple Taiwanese and a Wallacean origin, these results also contradict an influential “slow boat” model for Polynesian origins that suggests an ancestry in Taiwan at 4 ka for the maternal line of descent while positing a large Near Oceanic origin for the male side, based on Y chromosome evidence.[10], [47], [48] and [49] Our results suggest instead that the mtDNA subclade B4a1a and the major Pacific Y chromosome haplogroup C2 might be distributed in a rather similar way, with a proximally Near Oceanic, but ultimately Southeast Asian, ancestry. Several widely distributed paternal subclades may have a Taiwanese ancestry, but they only occur in Oceania at low frequencies.[49] and [50] Available autosomal microsatellite diversity, furthermore, suggests that Polynesian patterns show a partly East Asian and partly Near Oceanic ancestry at low resolution but are distinct from both at higher resolution.[51] and [52] This is also compatible with our model of a largely ancient Asian ancestry for Polynesian origins, with an early Holocene incubation period in ISEA and then in Near Oceania. The male and female lines of descent may therefore not have such radically contrasting histories as some have proposed.[10] and [53]

The spread of B4a1a1a back through New Guinea into ISEA, which most likely took place 4–5 ka, suggests instead that models based on the idea of a “voyaging corridor,”[5] and [7] facilitating exchange between ISEA and Near Oceania, may provide a more plausible backdrop to the settlement of the Remote Pacific. The HVS-I database provides further indications of small-scale bidirectional movements across this region. E1b, in particular, might plausibly have been carried by small numbers of Austronesian-speaking voyagers who integrated with coastal-dwelling B4a1a1 groups in the Bismarcks (where it is present at 5%), perhaps stimulating the rise and spread of the Lapita culture and the dispersal of the Oceanic languages.38 Other lineages from Southeast Asia are also found at low frequencies in Near Oceania, and still others are candidates for dispersal from Taiwan into eastern Indonesia via the Philippines, but they did not reach Oceania.25 Some of these may have also been involved in the transmission of Austronesian culture and languages, although they evidently had no demic role in the founding of Polynesia.

Thus, although our results rule out any substantial maternal ancestry in Taiwan for Polynesians, they do not preclude an Austronesian linguistic dispersal from Taiwan to Oceania 3–4 ka,54 mediated by social networks rather than directly by people of Taiwanese ancestry but perhaps involving small numbers of migrants at various times.9 The mtDNA patterns point to the possibility of a staged series of dispersals of small numbers of Austronesian speakers, each followed by a period of extensive acculturation and language shift.55

Overall, though, the mtDNA evidence highlights a deeper and more complex history of two-way maritime interaction between ISEA and Near Oceania than is evident from most previous accounts.54 Archaeological and linguistic evidence for maritime interaction between ISEA and Near Oceania during the early and mid-Holocene is strengthening, however,[9] and [56] and it has been suggested that contacts might have been facilitated by sea-level rises and improvements in conditions on the north coast of New Guinea.4 Early to mid-Holocene social networks between New Guinea and the Bismarck Archipelago are marked by the spread of stone mortars and pestles, obsidian, and stemmed obsidian tools from 8 ka57 until before or alongside the advent of Lapita pottery in the Bismarcks at 3.5 ka.6 The absence of early Lapita pottery on New Guinea suggests major disruptions to preexisting exchange networks within Near Oceania before or at 3.5 ka, with increasing social isolation of some areas and increasing interaction between others.

There is also emerging evidence from both archaeology and archaeobotany for the spread of domesticates during the mid-Holocene, before the presumed advent of Austronesian dominance from 4 ka. Molecular analyses suggest that bananas,58 sago,59 greater yam,60 and sugarcane61 all underwent early domestication in the New Guinea region. These cultivars, and associated cultivation practices, diffused westward into ISEA, where the plants and linguistic terms for them were adopted by Proto-Malayo-Polynesian speakers upon their arrival 4 ka[9], [54] and [62]. The vegetative cultivation of these plants evidently occurred within ISEA before any Taiwanese influences became significant.

This work suggests, therefore, a convergence of archaeological and genetic evidence, as well as concordance between different lines of genetic evidence. Our results imply an early to mid-Holocene Near Oceanic ancestry for the Polynesian peoples, likely fertilized by small numbers of socially dominant Austronesian-speaking voyagers from ISEA in the Lapita formative period, 3.5 ka. Our work can therefore also pave the way for new accounts of the spread of Austronesian languages.